Methane (CH4) is a greenhouse gas, and paddy fields are one of its main anthropogenic sources. In Japan, country-specific emission factors (EFs) have been applied since 2003 to estimate national-scale CH4 emission from paddy field. However, these EFs did not consider the effects of factors that influence CH4 emission (e.g., amount of organic C inputs, field drainage rate, climate) and can therefore produce estimates with high uncertainty. To improve the reliability of national-scale estimates, we revised the EFs based on simulations by the DeNitrification-DeComposition-Rice (DNDC-Rice) model in a previous study. Here, we estimated total CH4 emission from paddy fields in Japan from 1990 to 2010 using these revised EFs and databases on independent variables that influence emission (organic C application rate, paddy area, proportions of paddy area for each drainage rate class and water management regime). CH4 emission ranged from 323 to 455 kt C yr(-1) (1.1 to 2.2 times the range of 206 to 285 kt C yr(-1) calculated using previous EFs). Although our method may have overestimated CH4 emissions, most of the abovementioned differences were presumably caused by underestimation by the previous method due to a lack of emission data from slow-drainage fields, lower organic C inputs than recent levels, neglect of regional climatic differences, and underestimation of the area of continuously flooded paddies. Our estimate (406 kt C in 2000) was higher than that by the IPCC Tier 1 method (305 kt C in 2000), presumably because regional variations in CH4 emission rates are not accounted for by the Tier 1 method. (C) 2017 Elsevier B.V. All rights reserved.